Thanks everyone for your thoughts.

We need to move her upstairs at night as the house is alarmed downstairs. Also, when we start to leave her when we go out she will need to go upstairs (again - because of the alarm) so we want to get her used to it - eventually we want her have the run of one of the rooms upstairs when we're out/at night.

Good news though , we had a good night last night with different tactics! I think moving the crate is unsettling her so we're going to leave it upstairs from now on (Vikegirl - the crate is a collapsable one and isn't that heavy so is easy to move about). Last night we put it at the other side of our bedroom and put a hot water bottle in there for her to make it cosy. We also put a ticking clock next to it to soothe her and I sprayed some DAP spray in there (replicates pheromones produced by mum and helps calm them). When we went to bed she settled in there nearly straight away and slept through all night, no crying! We didn't close the door - that's something we've decided to build up to slowly once she's happy in there and comes to see it as her own safe place.

We're planning to move it a bit each night until she's in the other room - fingers crossed!

She seems a lot happier today anyway and is full of beans. I think some dogs are just more sensitive than others and closing the crate door and leaving her just made her get herself into a state.

Incidentally, I spoke to the vet yesterday and she said that the pooing in the night thing would stop once she gets a bit older and can control herself more. She was a dog owner and said she hadn't got up to let them out in the night and that they'd grown out of it pretty quick. Although I'm guessing toilet training will be quicker if you do let them out in the night.